Bruce Deagle

May 7, 2024  -  A paper has been published by Madi Green based on work done during her postdoctoral project which focussed on developing environmental DNA methods to reconstruct fisheries catch. In the published work Madi sampled brine water from fisheries vessels in the Australian Eastern Tuna Billfish Fishery. In this experiment it was possible to validate eDNA results with reliable catch data (consisting of seven target and bycatch species). Several other research groups have been doing similar work to evaluate eDNA's potential to become a new fisheries monitoring tool. The paper is available here.

Feb 25, 2024  -  We've received funding through the National Environmental Science Program (NESP) to further develop environmental DNA (eDNA) research being carried out as part of the South-East Australian Marine Ecosystem Survey (SEA-MES). The project involves the collection/analysis of eDNA samples from the RV Investigator on two voyages (July 2023 and May 2024) and will allow comparison biodiversity datasets we collect with more traditional survey methods (trawl net, deep-tow camera, acoustics). The overall aims are to examine how much biodiversity survey data can be collected with eDNA and to optimise eDNA sampling methods for ship-based surveys in offshore marine areas.  

A summary of the project is provided on the NESP website (Project 4.23 Environmental DNA for measuring offshore marine biodiversity: what can DNA in water collected from the RV Investigator tell us?).

Dec 15, 2023  -  A new book titled 'Applied Environmental Genomics' from CSIRO publishing was released recently. I contributed to Chapter 4 on 'Revealing animal diet and food-webs though DNA metabarcoding' with co-authors Johan Pansu, Julie McInnes and Michael Traugott. Two post-doctoral researchers from our team in the the CSIRO fish collection, Katrina West and Floriaan Delvoo-Delva, also contributed to chapters on eDNA (Chapter 5) and molecular sex identification (Chapter 8) respectively.

Click on the image below to get a preview of the book - or order your copy here  (link to CSIRO publishing website).

Dec 10, 2023  - Katrina, Floriaan and I from the CSIRO fish collection team recently attended the annual science meeting of CSIRO's Environomics Future Science Platform in Sydney. The Environomics FSP is a CSIRO initiative facilitating collaboration in environmental genomic research within CSIRO and with researchers in the university sector. The meeting consisted of many interesting and inspiring talks over three days covering advances in a range of topics, from eDNA methods to epigenetics and genomics. Katrina presented work comparing day/night eDNA signals at coastal Tasmanian sites and contrasted findings with data from diver visual surveys carried out at the same time. Florian presented work on methylation of DNA in Antarctic toothfish populations, this work is part of an FSP funded project investigating if methylation patterns obtained in tissues from this commercially harvested fish can be used to trace which part of the Southern Ocean the fish was caught in. Thanks very much to Olly Berry, Mark Wallace and others who helped organise the great meeting. 

Nov 15, 2023  - Today a publication led by CSIRO post-doc Maarten De Brauwer was released, the document is a roadmap for integration of environmental DNA (eDNA) science into Australian marine park monitoring. It outlines applications of eDNA technology for measuring biodiversity in marine parks; primary uses include monitoring changes in biological community structure at an ecosystem-wide level and early detection of potentially invasive species.

Using Maarten's words:

 "The roadmap aims to facilitate and streamline the integration of eDNA methods in marine parks and is the result of three years of consulting with marine park managers, monitoring teams, ecologists, policy makers, and molecular scientists. As such, the roadmap is based on both the needs and priorities of marine parks managers and a realistic assessment of current and future eDNA capacity in Australia"

You can find the detailed document in link below, but for a shorter read, a factsheet is here, and here's a conversation article.

July 25, 2023  -  Last week I was in Melbourne at the International Congress of Genetics for many fantastic presentations on a huge range of genetic research topics. I presented an overview work I've been involved in on DNA diet analysis as part of a session on Environmental Genomics (organised by Elise Furlan & Toshifumi Minamoto). I was joined at the conference by Floriaan Devloo-Delva (post-doc in the CSIRO fish collection) who presented work from his PhD on genetic sex-determination in sharks and rays. It was also a great opportunity to catch-up with many other CSIRO genetic researchers from other sites around Australia.

June 3, 2023  -  Last week I was in the field with CSIRO post-doctoral researcher Katrina West collecting eDNA from seawater at sites around Lord Howe Island. This island is a crossroads of marine biodiversity with a mixture of temperate, subtropical, and tropical species. Marine species have colonised the area from both cool southern ocean currents and the warm East Australian Current. Katrina's project is taking advantage of one of the strengths of eDNA analysis - the ability to characterise ecosystem-wide biodiversity - to study tropical-temperate transition sites off both the east and west coasts of Australia.

March 23, 2023  -  Translocations of the endangered Swan galaxias (Galaxias fontanus) were carried out this week as part of a project we are involved in. The species currently has healthy populations in only small parts of a few streams in eastern Tasmania. It was very exciting to have this fish moved to two new locations where it will hopefully flourish and provide a more promising long-term outlook for the species. Charlotte Jense and I collected some eDNA from the sites to see how much population genetic data can be extracted from a water sample. If the approach works, future genetic surveys could be done without disturbance to fish.

March 3, 2023  -  A huge amount of effort has gone into sequencing the Antarctic Krill genome and a paper summarising this project has just been been published . The work was led by Changwei Shao and a team of researchers from China with contributions from scientists based in Australia, Germany, Italy and Denmark. This genome sequencing project was technically challenging since the genome is comprised of 48 billion base pairs (it's the largest animal genome ever to be sequenced) and the gene coding regions are buried in vast regions of repetitive sequences (short repeats and transposable elements). Thanks to an extremely large amount of data from new DNA sequencing technology, advanced bioinformatics and a skilled team this valuable resource is now available for the scientific community. See paper here. A general summary of the paper is also available (BGI website article). 

Feb 20, 2023  -  There was a great environmental DNA (eDNA) conference in Hobart last week - many interesting talks and so many people using eDNA in their research. Also impressed by the involvement of commercial eDNA companies (and conference sponsors) providing not only eDNA services, but also involved in innovative research and pushing the field forward. A big thanks to Olly Berry and CSIRO for making this happen. Katrina West from our team who was involved in organisation of the event with the organising committee.

Jan 22, 2023  -  A paper led by Leonie Suter looking at environmental DNA  (eDNA) detection of Antarctic krill was published today. One of the challenges with using eDNA in surveys of common organisms is that  it isn't possible to distinguish if a signal comes from recent presence of the species, or if it is remnant DNA shed from organisms in the past. In order to distinguish between these two signals Leonie looked at DNA fragment sizes in the water,  with old eDNA expected to be more fragmented. First, to test if old DNA could be identified, an experiment was set up in the Australian Antarctic Division krill aquarium. Krill were allowed to live in the aquarium for a few days before being removed, then the eDNA signal monitored for several weeks. As expected, old DNA was  found to be more fragmented. This model of how DNA degrades was used to classify eDNA signals from Southern Ocean samples as being recent or old. The paper is available here and a link to an article summarising the work is below. 

Jan 16, 2023  -  We are involved in more conservation genetic research on the Swan galaxias (Galaxias fontanus). This Tasmanian endangered freshwater fish was identified as a Priority species in Australian governments Threatened Species Action Plan 2022-2032. Previously we documented the genetic diversity in the few remaining disjunct populations of the species (see update below from May last year) to identify priority populations for conservation. In the current project the CSIRO team and University of Tasmania PhD student Charlotte Jense are developing environmental DNA (eDNA) markers for use in mapping/monitoring the species distribution. A goal of the broader project is to undertake translocations (i.e. move some fish to new streams) to establish new populations.  For this part of the project we will also be using eDNA testing as one tool to help confirm that streams being considered for translocations are free of brown trout (Salmo trutta) - introduced brown trout are the primary cause of Swan galaxias decline.

Dec 9, 2022  -  I was on a marine science voyage in October (IN2022_V08) collecting environmental DNA samples to study biodiversity. There were a large number other projects and interesting discoveries - including amazing fine-scale mapping of seamounts and a surprise trawl which contained hundreds of sharks teeth! Now other members of the CSIRO fish collection are on board  the RV Investigator in another biodiversity survey (IN2022_V09) - this voyage is in Gascoyne Marine Park off the coast of Western Australia. Will White, John Pogonoski and Helen O'Neill  from our team are involved in collecting/identifying fish during this extensive survey. A news story covering findings from both voyages is in the link below.

Oct 4, 2022  - I am taking part in an expedition (IN2022_V08)  onboard CSIRO’s Marine National Facility (RV Investigator) to Australia’s Indian Ocean Territories (IOT). We'll be exploring deep ocean and seamounts around the remote Cocos (Keeling) Islands, which is home to a large new Australian marine park. A voyage last year (IN2021_V04) surveyed a neighbouring marine park surrounding Christmas Island.  These parks were announced last year, and will help protect an massive area of 740,000 square kilometres. The voyage will map seamounts and provide some of the first samples of  biodiversity from the depths of the marine park. I will be collecting eDNA samples that will be used as a small part of the biodiversity assessment - these samples will form part of Katrina West postdoctoral project. Katrina collected eDNA samples on the other leg of the voyage in July 2021. The CSIRO fish collection taxonomic/curatorial staff play a critical part in the identification and curation of fish specimens. John Pogonoski and Al Graham went on the first voyage, and are integral support for the fish collections on this voyage being led by taxonomists from Museums Victoria and Australian Museum 

Museums Victoria Research Institute (MVRI) is leading a voyage and has  some great information on the voyage and science objectives in the link below. 

Sept 7, 2022  - A study on the rare Maugean skate led by researchers at the Institute for Marine and Antarctic Studies (IMAS) is summarised  in a new report. The study set out to detect the presence of Maugean skate by looking for DNA from the species in Bathurst Harbour on the west coast of Tasmania (where the skate was originally found in the 1980's). Unfortunately the survey did not reveal a significant skate DNA signal meaning the only known population is in Macquarie Harbour on the west coast of Tasmania. Click  picture below for the press release, or see the report for more information. 

July  22, 2022  - We just received a large amount of data from a few environmental DNA (eDNA) projects I have been working on with Katrina West and others. Samples include eDNA Katrina collected on an Investigator voyage and other eDNA from Tasmania. We extracted DNA and PCR amplified two DNA barcode markers at the CSIRO genetics laboratory - then sent the library for NovaSeq sequencing at AGRF.

This data includes over 30 million sequences from a year of water collections at Tinderbox Marine Reserve - hopefully some will match the fish observed while snorkelling at the site! 

June  15, 2022  - Some excitement today as a devilray was found on a beach in Eastern Tasmania. Will White and Helen O'Neill  from our team drove to Coles Bay to pick it up and it was unloaded with a forklift outside the CSIRO fish collection to get as much information as possible from the specimen. The species is Mobula mobular  (Japanese Devilray). It  is not often seen this far south and unfortunately for this one the cool Tasmanian waters probably don't have suitable concentrations of food at this time of year . This fish is rarely found in museum collections and we could not keep the whole specimen since it was too large to fit into any of our storage tanks. Will and Helen did take detailed photographs, measurements, taxonomically informative skeletal samples and tissues for genetic analysis.

June , 2022  - A news story covering the CSIRO fish collection is in the link below. It includes a photos of potentially the ugliest fish in the collection and outlines covers some research activities our group is currently involved (shark egg cases and eDNA). 

May, 2022  - I produced a summary of recent work we've done on conservation genetics of the swan galaxias (Galaxias fontanus). This project is being carried out with biologists from Inland Fisheries Service Tasmania and collaborators from the University of Tasmania.  The genetic work was funded thorough the Bioplatforms Australia Threatened Species Initiative .

The Swan galaxias is an endangered freshwater fish with a severely fragmented distribution in headwater streams of two Tasmanian watersheds. Population connectivity is restricted by the downstream presence of introduced fish species. We provide the first assessment of genetic diversity in natural populations and evaluate how well diversity is preserved in translocated populations.  We also carried out genome sequencing (PacBio® HiFi sequencing) and transcriptome sequencing on a single fish. All sequence data are available from the Bioplatforms Australia Threatened Species initiative data portal.

December, 2021  - I've been slow in providing updates since I started at CSIRO's Australian National fish collection, but here are a few pictures of activities. I'll provide some project updates in 2022!

May 30, 2021  - A paper by Julie McInnes et al. was recently published on a survey of burrowing seabirds using genetic species identification from discarded feathers and scats. As the name suggests these birds spend most of their life at sea but return to land and nest in burrows. While breeding they incubate eggs underground or forage at sea during the day, only moving in and out of burrows under the cover of darkness. Surveys of breeding numbers are possible through burrow cameras, spotlight surveys, capturing birds or by recording their distinctive calls - but it is still difficult to monitor the species of birds nesting in an particular area. This is where genetic approaches may be able to help.

This study was done on sub-Antarctic Macquarie Island where numbers and possibly diversity of burrowing seabirds are expected to increase following vertebrate pest eradication (see details on broader project here). Using feathers and scats collected near burrows Julie obtained high quality DNA for seabird identification, assisting in detection of new species arrivals and new breeding sites. More information can be found in the Paper Link.

April 7, 2021  - DNA sequences are now commonly used to identify species in studies of biodiversity. This is only possible when we have access to reference databases containing records with reliable taxonomy and matched high-quality DNA sequences. Barcode of Life Data Systems (BOLD) is a large and trusted database linking taxonomy with DNA sequences. With over 9 million barcoded specimens the curation of data is challenging.

I played a small role in curation of marine barcode data deposited in BOLD initiated during a workshop at the 8th International Barcode of Life Conference(workshop organised by Filipe Costa and Adriana Radulovici). Data from some of the major taxonomic groups (crustaceans, echinoderms, molluscs, and polychaetes) were examined to find potential data quality issues - i.e. incongruence between Linnaean names and Barcode Index Numbers (BINs).

Almost 40% of sequences (over 80,000) were flagged as needing curation, and these were manually reviewed. After review, we found a small proportion of these were due to specimens that were misidentified, mislabelled, or contaminated (3% of specimens). The remaining records were flagged due to other issues (multiple species that shared the same BIN, one species with multiple BINs, or the incongruence was ambiguous). The results highlight that data curation (preferably automated!) is crucial for ongoing DNA barcode applications. The findings been summarised in a new paper available here.

Jan 21, 2021  - Data on penguin diet collected by Andrea Polanowski and myself was published as part of a paper on Gentoo penguins from the sub-Antarctic island of South Georgia (paper link here). The project was led by Norman Ratcliffe, a penguin ecologist at British Antarctic Survey (BAS). The BAS team put out satellite trackers on birds to look at their foraging range and potential for overlap with the winter krill fishery in the area. They also collected poo samples for us to determine what the penguins were eating. One of the results of this research is that Gentoo penguins are now benefiting from a newly enlarged no-fishing zone around this sub-Antarctic island.

This paper has coverage on a number of websites, so you can read more at these links:

British Antarctic Survey - news story

The Pew Charitable Trusts - news story

Australian Antarctic Division - news story

Also the penguin foraging routes recorded during the study can be seen here.

Jan 5, 2021  - A paper on geographic structuring of the bacterial communities that live on Antarctic krill has been published in the journal Molecular Ecology (paper link). This research (led by Laurence Clarke) found that krill‐associated bacterial communities are geographically structured, in direct contrast with the lack of structure observed in traditional population genetic studies of Antarctic krill. So, even though a species appears to be completely mixed based on their own genetics (i.e. a panmictic population) their associated bacterial communities can provide a distinctive signature in different parts of the species distribution. The current study showed that the differences between bacterial communities were best explained by distance (i.e. due to lack of ongoing bacterial dispersal) rather than environmental conditions. The research also showed that when krill from a single swarm are split between aquarium tanks in controlled conditions their krill‐associated bacterial communities diverge, presumably due to small random changes over time (i.e. drift). This field of research is relatively new, but could potentially be used to provide information on the stock structure of species for fisheries management and could provide novel insight into animal movement and population interactions.

Nov 30, 2020 - I gave a virtual talk as part of a International Virtual Conference on the use of Environmental DNA (eDNA) in Marine Environments that was run by the Partnership for Observation of the Global Ocean (POGO). A link to the video of the presentation is available here: recorded plenary talk (26 min)

Aug 7, 2020 - Further work from an Australian Antarctic Science project that is focused on genetics approaches to monitor Southern Ocean plankton diversity was recently published in the journal Molecular Ecology (paper link). A nice public summary is here. This paper was led by Leonie Suter and is based on samples collected while the Antarctic icebreaker Aurora Australis was underway on a resupply voyage to Macquarie Island (see story on sampling trip). In this paper we compared the zooplankton identified by sequencing environmental DNA (recovered from 2 litre water samples) with whole organisms collected by the Continuous Plankton Recorder that was being towed behind the ship. The take-home message from this paper is that even small water volumes taken from a moving ship can provide a rich view of plankton communities along the voyage track. Standardised sampling of environmental DNA on Southern Ocean resupply voyages would complement traditional approaches to monitor biodiversity and increase our understanding of zooplankton communities in this remote region. The Aurora Australis recently completed her last voyage with the Australian Antarctic program (story here) hopefully the new ship will collect environmental DNA as standard part of underway monitoring in the new era of Australian Antarctic Science. 

July 6, 2020 - A paper from recent PhD graduate Cathy Cavallo (Monash University) was just published (see paper here) - Cathy discussed the main results from her paper in an interview here. She worked with the AAD genetics group to collect DNA-based diet data from little penguins in breeding colonies at Phillip Island. This paper combined the diet data collected over two seasons with parallel data on trip duration and the weight of food the penguins collected for their chicks on each trip. Taken together this information provides a measure of how much effort is required by the penguins to capture different prey in a given season.

April, 2020 - I have started a new position as a CSIRO Science Leader and team leader at the Australian National Fish Collection. This is a shift from my focus over the last 9 years in the Australian Antarctic Program - an exciting opportunity to do research on Australian fishes in a large national science organisation. I'll still be based in Tasmania - photos I've taken of local fish diversity below: